Physics-based modeling of side chain - said chain interactions in the UNRES force field

Mariusz Makowski


Work on a development of a new model of side-chain—side-chain interactions for side-chains of amino acids, to be used in the UNRES force-field and in other large-scale simulations, has been described in this chapter. In the presented model a polar/charged side chain consists of two sites of interaction, nonpolar and polar. General expressions for the effective energy of interaction between amino acids are given depending on the kind of interacting pair. Results of tests with the new UNRES force-field parameters have also been shown together with an extension of the force-field for the phosphorylated amino-acids in this chapter. The results of the studies on the influence of particle size on the free-energy profile of hydrophobic interactions, and the temperature dependence of the potential of mean force for side chain—side chain interactions are also presented.
Author Mariusz Makowski (FCh / KChBionieorg. / LII)
Mariusz Makowski,,
- Laboratory of Intermolecular Interactions
Pages 89-115
Publication size in sheets1.3
Book Liwo Józef Adam (eds.): Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: from bioinformatics to molecular quantum mechanics, Springer Series on Bio- and Neurosystems, vol. 8, 2019, Springer, ISBN 978-3-319-95842-2, [978-3-319-95843-9], 851 p., DOI:10.1007/978-3-319-95843-9
Keywords in EnglishAmino acid side chains, model of side-chain-side-chain interactions, potential of mean force, phosphorylated amino-acids, hydrophobic interactions, temperature dependence, molecular dynamics, umbrella sampling
Languageen angielski
Score (nominal)5
ScoreMinisterial score = 5.0, 05-02-2019, BookChapterNotSeriesMainLanguages
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